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Utility of the Cryptosporidium oocyst wall protein (COWP) gene in a nested PCR approach for detection infection in cattle.

A preliminary molecular epidemiological study was carried out to investigate the utility of the Cryptosporidium oocyst wall protein (COWP) gene in the detection of Cryptosporidium oocysts in fecal samples. A nested polymerase chain reaction (PCR) approach using COWP gene primers was adopted for this purpose. Fecal samples were spiked with each of 1, 10, and 100 oocysts of C. parvum, four samples for each number, and the DNA was extracted from each sample using a glassbead method. The presence of oocysts was determined using the nested PCR with COWP gene primers, and the limit of detection of oocysts by the PCR was determined. The limit of detection was 100 oocysts spiked in 1 ml of fecal material (50% sold material) (four positives/four samples tested). Seventy-five percent of DNA extracted samples spiked with 1 and 10 oocysts was positive by the PCR (three positives/four samples tested). Based on this, small sample size using the COWP gene primers with a nested PCR analysis could reliably identify infected animals rather conveniently and accurately.

Animals↗

Mapping of ribosomal protein S3 and internally nested snoRNA U15A gene to human chromosome 11q13.3-q13.5.

The mammalian ribosome is a massive structure composed of 4 RNA species and about 80 different proteins. One of these ribosomal proteins, S3, appears to function not only in translation but also as an endonuclease in repair of UV-induced DNA damage. Moreover, the first intron of human RPS3 transcripts is processed to generate U15A, a small nucleolar RNA. We localized the nested RPS3/U15A genes to the immediate vicinity of D11S356 and D11S533 on human chromosome 11q13.3-q13.5 using a combination of somatic cell hybrid analysis, fluorescence in situ hybridization, and YAC/STS content mapping. These findings add to the evidence that genes encoding ribosomal proteins are scattered about the human genome.

Animals↗

Phylogenetic analysis of spotted fever group rickettsiae based on gltA, 17-kDa, and rOmpA genes amplified by nested PCR from ticks in Japan.

In order to understand the natural situation of rickettsiae in the ticks in Japan, the rickettsial genes, gltA gene, rOmpA gene, and 17-kDa gene, were amplified from the ticks by nested PCR. The prevalences of rickettsial gltA genes among Haemaphysalis formosensis, H. longicornis, H. megaspinosa, Ixodes ovatus, H. flava, H. kitaokai, and I. persulcatus were 62, 57, 24, 24, 19, 13, and 10%, respectively; 26% (186/722) being the average. The gltA genes amplified from the ticks were classified into 9 genotypes (I to IX) by the difference in nucleotide sequences. Genotype I was detected from 7 species of ticks. Genotype II mainly was detected from H. longicornis and H. formosensis. Genotypes III and VII mainly were detected from H. flava and I. ovatus. The polarization in the distribution of genotypes among regions where the ticks were collected was not clear. Based on the phylogenetic analysis of the three genes presented here, genotypes I, III, and IV (detected from H. formosensis, H. hystricia, and I. ovatus ) are genetically close with each other, but rickettsiae of the same property still have not been isolated from ticks anywhere in the world. These genotypes should be considered as new species among SFG rickettsiae. Genotype II was identical with strain FUJ-98, genetically close to R. japonica which has been isolated from ticks in China. Genotype V was identical with R. felis and strain California 2 isolated from the cat flea. This is the first report on the detection of R. felis from ticks. Genotype VI detected from Ixodes sp. did not seem to belong to genus Rickettsia. Based on the previous antigenic data and the phylogenetic analysis presented here, Genotype VII should be considered a variant of R. helvetica and genotype VIII detected from I. ovatus and I. persulcatus were identical with R. helvetica. Genotype IX detected from I. nipponensis was genetically close to the strains IRS3, IRS4, and IrR/Munich isolated from I. ricinus in Slovakia and German.

Animals↗

Detection of streptococcal pyrogenic exotoxin genes by a nested polymerase chain reaction.

Severe invasive disease associated with group A Streptococcus (GAS) has recently increased in frequency. Isolates of GAS from normally sterile sites were examined for the streptococcal pyrogenic exotoxin genes spe A, spe B and spe C to determine if they play a role in this disease. Four primers for each gene were used in a nested polymerase chain reaction (PCR) configuration. The first PCR generated fragments of 818, 1106, and 801 bp, respectively, for the extotoxin genes. The second PCR generated fragments of 500, 912 and 654 bp for the spe A, spe B and spe C genes using the fragments from the first PCR as template. Of 62 strains tested, 35 (56%) contained the spe A gene, and 17 (27%) contained the spe C gene. All GAS strains studied, regardless of disease association, contained the spe B gene. These data corroborate accumulating evidence that the genes encoding pyrogenic exotoxin types B and C are not associated with severe invasive streptococcal illness including streptococcal toxic shock-like syndrome. This PCR-based gene detection system has clinical and epidemiologic applications because of its ease of performance, non-isotope labelling, high specificity and sensitivity, and lack of requirement for purified DNA.

Bacterial Proteins↗

GATA-6 gene enhancer contains nested regulatory modules for primary myocardium and the embedded nascent atrioventricular conduction system.

The cGATA-6 gene is flanked by an enhancer that selectively marks the atrioventricular conduction system (AVCS) in transgenic mice. This enhancer reads anterior/posterior and medial/lateral positional information very early in the cardiogenic program and remains active in progressively more restricted regions of primary myocardium leading up to the emergence of a histologically distinct AVCS. We undertook to parse this enhancer to resolve how the respective AVCS-specific transcription program is regulated at the molecular level. We determined that this AVCS enhancer includes a 102 bp module that is sufficient to restrict expression to primary nonchamber myocardium. This offers a novel tool to analyze the early molecular delineation of primary and chamber myocardium, which subsequently give rise to components of the central and peripheral conduction system, respectively. Furthermore, we show that this 102 bp module in turn contains a nested 47 bp core module that has the potential to direct expression specifically to the AVCS domain of primary myocardium, albeit with low efficiency. Accordingly, we show that a GATA site and a GC-rich site in the 102 bp region bolster the activity of the nested 47 bp AVCS core region even within the context of the parental 1,478 bp enhancer. These are the first functional elements to be reported for a cardiac conduction system-specific control region.

Animals↗

Molecular genetic analysis of the nested Drosophila melanogaster lamin C gene.

Lamins are intermediate filaments that line the inner surface of the nuclear envelope, providing structural support and making contacts with chromatin. There are two types of lamins, A- and B-types, which differ in structure and expression. Drosophila possesses both lamin types, encoded by the LamC (A-type) and lamin Dm0 (B-type) genes. LamC is nested within an intron of the essential gene ttv. We demonstrate that null mutations in LamC are lethal, and expression of a wild-type LamC transgene rescues lethality of LamC but not ttv mutants. Mutations in the human A-type lamin gene lead to diseases called laminopathies. To determine if Drosophila might serve as a useful model to study lamin biology and disease mechanisms, we generated transgenic flies expressing mutant LamC proteins modeled after human disease-causing lamins. These transgenic animals display a nuclear lamin aggregation phenotype remarkably similar to that observed when human mutant A-type lamins are expressed in mammalian cells. LamC aggregates also cause disorganization of lamin Dm0, indicating interdependence of both lamin types for proper lamina assembly. Taken together, these data provide the first detailed genetic analysis of the LamC gene and support using Drosophila as a model to study the role of lamins in disease.

Alleles↗

Typing class I HLA-A gene using a nested PCR-RFLP procedure.

In order to detect several new HLA-A class I alleles that have been described since 1998, the original PCR-RFLP method developed to identify the 78 alleles recognized at that time at high resolution level was adapted by us for low and medium resolution levels using a nested PCR-RFLP approach. The results obtained from blood samples of 23 subjects using both the PCR-RFLP method and a commercial kit (MicroSSP1A, One Lambda Inc.) showed an agreement higher than 95%. The PCR-RFLP adapted method was effective in low and medium resolution histocompatibility evaluations.

Alleles↗

Nested PCR allows the characterization of TaqI and PstI RFLPs in the second exon of the caprine MHC class II DRB gene.

A nested polymerase chain reaction (PCR) method has been developed to obtain a specific amplification of the second exon of the caprine MHC class II DRB gene. The specificity of this method has been verified by cloning and sequencing the PCR product and comparing its sequence to 21 previously published caprine DRB second exon allelic variants. Nucleotide identity between this sequence (Caae-DRB23) and other caprine DRB alleles ranged between 85.6% (Caae-DRB22) and 96.5% (Caae-DRB5). Caae-DRB5 and Caae-DRB23 sequences diverged in five amino acid substitutions (70, 71, 73, 74, 78), all of them placed at the antigen binding site. Likewise, the restriction polymorphism of the caprine DRB second exon has been analyzed and two different restriction patterns have been found depending on the presence or absence of a TaqI site and a PstI site at positions 122 bp and 241 bp of the PCR product respectively. TaqI and PstI RFLPs were also analyzed in other artiodactyla species. While PstI RFLP was found not only in goats but also in cattle, sheep and pigs, TaqI RFLP was only detected in goats. In all of these species close associations were detected between the presence of TaqI and PstI restriction sites and amino acid substitutions at positions 40 and 78 respectively, suggesting that PCR restriction fragment length polymorphism (RFLP) could be a useful tool in relating amino acid substitutions at critical positions with disease resistance.

Amino Acid Sequence↗

Cloning of chicken choline acetyltransferase and its expression in early embryonic retina.

The enzyme choline acetyltransferase [EC 2.3.1.6] (ChAT) synthesizes the neurotransmitter acetylcholine that plays a key morphogenic role in vertebrate retina development. As the embryonic avian retina is particularly useful for morphogenetic studies, we cloned the complete coding region of chicken ChAT cDNA. At the deduced amino acid level, chicken ChAT is approximately 76% identical to mammalian ChAT proteins. We also report here the cloning of the complete 5' end of the complex cholinergic locus. This locus contains both the ChAT gene and the nested intronless gene for the vesicular acetylcholine transporter (VAChT). The genomic organization of the 5' end of the chicken cholinergic locus is similar to that reported in other vertebrate species. A 5.7 kb mRNA corresponding to the ChAT message was detected in both embryonic retina and post-hatch brain. An analysis of the ChAT mRNA in embryonic chick retina shows that the message can be detected by E6 and its level increased during early retinal development. Vertebrate ChAT mRNAs can contain one or more of three non-coding exons, M, N or R and by RT-PCR we demonstrate, at least, a chicken ChAT mRNA containing exon M.

Amino Acid Sequence↗

Regulation of two nested proteins from gene 49 (recombination endonuclease VII) and of a lambda RexA-like protein of bacteriophage T4.

Phage T4 gene 49, encoding recombination endonuclease VII, specifies, by initiation from an AUG and an internal GUG codon, two in-frame overlapping peptides (of 18 and 12 kD). The gene is transcribed early and late, albeit from different promoters. The sequence predicts that in long early transcripts, initiated far upstream of the coding sequence, the Shine-Dalgarno sequence of the first ribosome binding site can be sequestered in a hairpin and/or cleaved. These processes might reduce initiation from the first AUG and facilitate initiation of the 12-kD peptide from the internal GUG. The potential of this hairpin to participate in Y structures or cruciforms suggests possible autoregulation. Shorter, more stable late transcripts initiated from a late promoter immediately upstream of the first ribosome binding site cannot form this hairpin. More efficient translation of the longer 18-kD gene 49 peptide from these late transcripts accounts for the strong dependence of endonuclease VII activity on late gene expression. An ORF downstream from gene 49 can be translated from a motA-dependent transcript that starts inside gene 49 as well as from the gene 49 transcripts. Its initiation codon overlaps the stop codon of gene 49, suggesting some coupling of translation. The deduced protein resembles, among others, the RexA protein of phage lambda. Possible implications for T4 recombination and for the interference of lambda lysogens with T4 gene 49 and rII mutants are discussed.

Amino Acid Sequence↗

The structural genes for alpha 1 and alpha 2 chains of human type IV collagen are divergently encoded on opposite DNA strands and have an overlapping promoter region.

Many of the genes of simple organisms with small genomes are encoded on opposite DNA strands so that the genes either overlap or one gene is nested within another gene (Normark, S., Bergström, S., Edlund, T., Grundström, T., Jaurin, B., Lindberg, F.P., and Olsson, D. (1983) Annu. Rev. Genet. 17, 499-525; Chen, C., Malone, T., Beckendorf, S.K., and Davis, R.L. Nature (1987) 329, 721-724). In contrast, most of the genes of complex organisms are dispersed in the genome in widely separated locations. Here, we report that the genes for the alpha 1 and alpha 2 chains of human type IV collagen are encoded on opposite DNA strands from loci that are so closely located that they may be separated by as little as 42 base pairs. The results provide the first description of two structural genes from a complex organism that code for two polypeptide chains of the same protein molecule but have overlapping 5'-flanking regions.

Amino Acid Sequence↗

Genomic structure and sequence of the pufferfish (Fugu rubripes) growth hormone-encoding gene: a comparative analysis of teleost growth hormone genes.

A nested polymerase chain reaction (PCR) technique for amplifying a fragment of the gene (GH) encoding teleost growth hormone has been developed. Using this technique, a fragment of the pufferfish, Fugu rubripes and Arothron maculatus, dwarf gourami, Colisa lalia; guppy, Poecilia reticulata; and goldfish, Carassius auratus GH genes were cloned. The Fugu rubripes (Fugu) gene fragment was used to isolate the GH gene from a Fugu genomic library. The complete nucleotide sequence of a 8.5-kb SacI genomic fragment containing the Fugu GH gene has been determined. The GH gene spans 2.5 kb from the first codon to polyadenylation signal, and contains six exons and five introns similar to the GH genes of salmonids, tilapia, barramundi, flounder and yellowtail. The GH introns contain microsatellite and satellite sequences. The microsatellites found in the fifth intron of the GH gene are also present in the corresponding introns of tilapia, barramundi and flounder GH genes. Southern analysis revealed that the GH gene is a single-copy gene in the Fugu. The promoter region of the Fugu GH gene contains conserved sequences that are likely to be involved in the pituitary-specific expression of the gene. A phylogenetic tree of nucleotide (nt) sequences of all known teleost GH genes has been inferred using the distance matrix method. The topology of this tree reflects the major phylogenetic groupings of teleosts. The intron patterns and repetitive sequences of GH genes can serve as useful natural markers for the classification and phylogenetic studies of teleosts.

Amino Acid Sequence↗

The prevalence of Borrelia burgdorfieri (Spirochaetales: spirochaetaceae) and the agent of human granulocytic ehrlichiosis (Rickettsiaceae: Ehrlichieae) in Ixodes scapularis (Acari:Ixodidae) collected during 1998 and 1999 from Minnesota.

We tested 103 adult Ixodes scapularis Say from 12 counties in Minnesota for the presence of Borrelia burgdorferi and the causative agent of human granulocytic ehrlichiosis (HGE), using polymerase chain reaction (PCR). A total of 17 ticks (16.5%) was positive for B. burgdoiferi using nested PCR for the flagellin gene. or both PCR for the ospA gene and nested PCR for the flagellin gene. A total of four ticks (3.8%) was positive for the agent of HGE using nested PCR for 16S rDNA. Counties in Minnesota with established and recently reported populations of I. scapularis both had ticks infected with B. burgdorferi. The agent of HGE was only detected in counties with established I. scapularis populations.

Anaplasmataceae↗

Further analysis of a transcript nested within the actin 5C gene of Drosophila melanogaster.

Previously we uncovered a 0.45-kb transcript within the 3' end transcribed untranslated region (3'UTR) of actin gene at 5C3-4 (act5C) of Drosophila melanogaster. We report here that its sequence bears no similarity to the known DNA or protein sequences. This and act5C transcripts are loaded on different polyribosomal classes. Gel retardation experiments performed with this fragment and several others from act5C reveal no DNA binding activity. The 0.45-kb transcript, initially isolated from different developmental stages of D. melanogaster embryogenesis, is also expressed in Drosophila Kc tissue culture cells, which will be used in transformation experiments designed to identify regulatory features of the nested gene and its possible interaction at some level with its "host" act5C gene.

Actins↗

A novel snoRNA (U73) is encoded within the introns of the human and mouse ribosomal protein S3a genes.

The mouse ribosomal protein S3a-encoding gene (mRPS3a) was cloned and sequenced in this study. mRPS3a shares identical exon/intron structure with its human counterpart. Both genes are split to six exons and exhibit remarkable conservation of the promoter region (68.8% identity in the 250 bp upstream of cap site) and coding region (the proteins differ in two amino acids). mRPS3a displays many features common to other r-protein genes, including the CpG-island at 5'-end of the gene, cap site within an oligopyrimidine tract and no consensus TATA or CAAT boxes. However, mRPS3a represents a rare subclass of r-protein genes that possess a long coding sequence in the first exon. Comparison of human and mouse S3a genes revealed sequence fragments with striking similarity within introns 3 and 4. Here we demonstrate that these sequences encode for a novel small nucleolar RNA (snoRNA) designated U73. U73 contains C, D and D' boxes and a 12-nucleotide antisense complementarity to the 28S ribosomal RNA. These features place U73 into the family of intron-encoded antisense snoRNAs that guide site-specific 2'-O-ribose methylation of pre-rRNA. We propose that U73 is involved in methylation of the G1739 residue of the human 28S rRNA. In addition, we present the mapping of human ribosomal protein S3a gene (hRPS3a) and internally nested U73 gene to the human chromosome 4q31.2-3.

Amino Acid Sequence↗

Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in Fugu.

The genes encoding synapsin (Syn) and the tissue inhibitor of metalloproteinase (Timp) exhibit a nested organization that is conserved in fruit fly and vertebrates. Analysis of the human and Fugu genomes show that the evolution of Syn-Timp gene families is characterized by duplications, secondary loss and the partitioning of ancestral functions. Of particular interest are two duplicate Syn-Timp loci in Fugu that have accumulated complementary degenerate mutations such that each Syn duplicate produces one of the two transcripts generated from the single ancestral gene, and one of the Timp genes is lost.

Alternative Splicing↗

Short communication: retrospective study to time the introduction of HIV type 1 non-B subtypes in Lyon, France, using env genes obtained from primary infection samples.

Using blood samples from primary HIV-1 infection (PHI) patients obtained in Lyon, France, we characterized the newly transmitted HIV-1 variants in this area during the 1992-1996 period. As PHI samples allowed the precise timing of the transmission event, we were able to date the introduction of non-B subtypes or recombinant forms of the virus in Lyon. Genomic DNA from 18 HIV-1-positive patients at primary infection was used to amplify the full-length env gene by nested PCR; after cloning, the gene was sequenced for subsequent phylogenetic analysis. Several non-B subtypes and recombinant forms of HIV-1 were identified among the 18 patients studied (1 subtype F1, 1 CRF01-AE, 2 subtype G and 2 CRF02-AG). We also found a new J/K recombinant form transmitted in 1995 and never described until now. The introduction of CRF02-AG in Lyon, France, occurred prior to 1992 and six transmission events including non-B subtypes were documented in the following 4 years. Heterosexual contacts appeared as the main introduction pathway for non-B subtypes or recombinant forms. Nevertheless, as transmission of these viruses occurred not only during travel to endemic regions, but also in France or Germany, we conclude that non-B strains entered Europe before the studied period. This retrospective study showed that even if subtype B remained prevalent in the spreading HIV-1 infection in Lyon between 1992 and 1996, non-B subtypes and circulating recombinant forms represented a significantly growing part.

Acquired Immunodeficiency Syndrome↗